As long as you use a JRE with support of the extension mechanism (Java < 1.9), you can still have some troubles but as we renamed some packages in JOGL (before doing the same in Java3D), it happens a lot less.

Actually, some end users go on reinstalling the Apple JRE to work around some limitations/bugs in the detection of the Java plugin but it causes much more problems...

Phil, I wrote in my tutorial that "disabling" the extension mechanism can have some nasty side effects, it breaks some features including NIO2 ZIP support. You should look at Emmanuel's source code, he creates a custom class loader. The best solution consists in bundling Java 1.9 as it has no extension mechanism :)

P.S: I use JNDT which isn't a proprietary black box with numerous limitations...